A lot more genes may separate humans from their chimp relatives than earlier studies let on. Researchers studying changes in the number of copies of genes in the two species found that their mix of genes is only 94 percent identical. The 6 percent difference is considerably larger than the commonly cited figure of 1.5 percent.
The new finding supports the idea that evolution may have given humans new genes with new functions that don't exist in chimps, something researchers had not recognized until recently. The older value of 1.5 percent is a measure of the difference between equivalent genes in humans and chimps, like a difference in the spelling of the same word in two similar languages. Based on that figure, experts proposed that humans and chimps have essentially the same genes, but differed in when and where the genes turn on and off.
The new research takes into account the possibility for multiple copies of genes and that the number of copies can differ between species, even though the gene itself is the same or nearly so. "You have to pay attention to more than just the genes that are shared," says geneticist Matthew Hahn of Indiana University, Bloomington, lead author of the new report. Researchers believe that additional copies of the same gene allow evolution to experiment, so to speak, finding new functions for old genes.
Hahn and his colleagues set out to study these gains and losses in gene number over the millennia by examining the genomes of humans, chimps, mice, rats and dogs. They looked at 110,000 genes that fall into 9,990 different families of similar genes.


The size of a gene family differed between species in 5,622 cases, or 56 percent of all the families. These size changes are so frequent in the evolutionary history of mammals that genes might as well be going through a revolving door, the researchers write in a paper published in a new online journal, PLoS ONE.
In humans and chimps, which have about 22,000 genes each, the group found 1,418 duplicates that one or the other does not possess. For example, humans have 15 members of a family of brain genes linked to autism, called the centaurin-gamma family, whereas chimps have six, for a difference of nine gene copies.

The group estimated that humans have acquired 689 new gene duplicates and lost 86 since diverging from our common ancestor with chimps six million years ago. Similarly, they reckoned that chimps have lost 729 gene copies that humans still have.

"The paper supports the emerging view that change in gene copy number, via gene duplication or loss, is one of the key mechanisms driving mammalian evolution," says genomics researcher James Sikela of the University of Colorado Health Sciences Center.